5Z2C

Crystal structure of ALPK-1 N-terminal domain in complex with ADP-heptose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

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This is version 1.2 of the entry. See complete history. 


Literature

Alpha-kinase 1 is a cytosolic innate immune receptor for bacterial ADP-heptose.

Zhou, P., She, Y., Dong, N., Li, P., He, H., Borio, A., Wu, Q., Lu, S., Ding, X., Cao, Y., Xu, Y., Gao, W., Dong, M., Ding, J., Wang, D.C., Zamyatina, A., Shao, F.

(2018) Nature 561: 122-126

  • DOI: https://doi.org/10.1038/s41586-018-0433-3
  • Primary Citation of Related Structures:  
    5Z2C

  • PubMed Abstract: 

    • Immune recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors often activates proinflammatory NF-κB signalling 1 . Recent studies indicate that the bacterial metabolite D-glycero-β-D-manno-heptose 1,7-bisphosphate (HBP) can activate NF-κB signalling in host cytosol 2-4 , but it is unclear whether HBP is a genuine PAMP and the cognate pattern recognition receptor has not been identified ...

    Immune recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors often activates proinflammatory NF-κB signalling 1 . Recent studies indicate that the bacterial metabolite D-glycero-β-D-manno-heptose 1,7-bisphosphate (HBP) can activate NF-κB signalling in host cytosol 2-4 , but it is unclear whether HBP is a genuine PAMP and the cognate pattern recognition receptor has not been identified. Here we combined a transposon screen in Yersinia pseudotuberculosis with biochemical analyses and identified ADP-β-D-manno-heptose (ADP-Hep), which mediates type III secretion system-dependent NF-κB activation and cytokine expression. ADP-Hep, but not other heptose metabolites, could enter host cytosol to activate NF-κB. A CRISPR-Cas9 screen showed that activation of NF-κB by ADP-Hep involves an ALPK1 (alpha-kinase 1)-TIFA (TRAF-interacting protein with forkhead-associated domain) axis. ADP-Hep directly binds the N-terminal domain of ALPK1, stimulating its kinase domain to phosphorylate and activate TIFA. The crystal structure of the N-terminal domain of ALPK1 and ADP-Hep in complex revealed the atomic mechanism of this ligand-receptor recognition process. HBP was transformed by host adenylyltransferases into ADP-heptose 7-P, which could activate ALPK1 to a lesser extent than ADP-Hep. ADP-Hep (but not HBP) alone or during bacterial infection induced Alpk1-dependent inflammation in mice. Our findings identify ALPK1 and ADP-Hep as a pattern recognition receptor and an effective immunomodulator, respectively.

    Organizational Affiliation: 

    Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China. shaofeng@nibs.ac.cn.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-protein kinase 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I
446Homo sapiensMutation(s): 0 
Gene Names: ALPK1, KIAA1527, LAK
EC: 2.7.11 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QP1 (Homo sapiens)
Explore Q96QP1 
Go to UniProtKB:  Q96QP1
PHAROS:  Q96QP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QP1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AYU
Query on AYU
Download Ideal Coordinates CCD File 
J [auth A]
K [auth B]
L [auth C]
M [auth D]
N [auth E]
J [auth A],
K [auth B],
L [auth C],
M [auth D],
N [auth E],
O [auth F],
P [auth G],
Q [auth H],
R [auth I]
[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4S,5S,6R)-6-[(1S)-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate
C17 H27 N5 O16 P2
KMSFWBYFWSKGGR-DTBZDYEHSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.26α = 90
b = 214.388β = 110.33
c = 173.151γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-19
    Changes: Data collection, Database references